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Abstract: Based on the Delft3D-FLOW, a 2D/3D hydrodynamic and sediment transport model was set up for the region of Yangtze Estuary, China. After a series of model verifications, which showed that the model is capable to reproduce the hydrodynamic and sediment transport processes in the region, it is applied to study the storm surge problem and morphological evolution of the Jiuduansha Shoals. It is concluded that the effects of remote wind and waves should be considered to obtain accurate results for storm surges. For reproducing the morphological changes the transport of cohesive as well as the non-cohesive fraction of sediment needs to be taken into account. The model can be considered as a basic tool for managing and studying the Yangtze Estuary. [Copyright &y& Elsevier]

Coastal ecosystems are strongly influenced by terrestrial inputs of freshwater, sediments, and nutrients, particularly in a megariver estuary of the Changjiang River. A remarkable increase in nutrient loading from the Changjiang River to the shelf has been observed over the period from 1999 to 2016 and turned the region into a high eutrophication condition. The Finite‐Volume Community Ocean Model and the European Regional Seas Ecosystem Model were coupled to assess the impact of the nutrient loading on the interannual variability of nutrients and phytoplankton. The model was first validated via observational data, and then dynamical analysis were conducted. Singular vector decomposition analysis indicated that the rapid change of local ecosystem was highly correlated with the change in river nutrient contributions. The Changjiang estuarine ecosystem was phosphate limited. The phosphate exhibited local variation, while the abundant nitrate from the river was diluted by the low‐nitrate oceanic water. The suspended sediment was significantly correlated with phytoplankton but not with nutrients. The ratio of diatom biomass to dinoflagellate biomass respected a rapid response to strong oscillations in the river nutrient input. High diatom primary production occurred near the sediment front, whereas the dinoflagellate bloom extended significantly offshore. The spring diatom and dinoflagellate blooms had major peaks in the empirical orthogonal function Modes 1 and 2, and the autumn bloom is characterized by secondary peaks from Mode 2 in the autumn. Plain Language Summary: There was an increase in the nutrient input into the Changjiang Estuary with an increased use of agricultural fertilizer as food demand rises globally. Further, there will be additional changes to river and estuary fluxes due to global anthropogenic activities in the future. This study presented the results of a novel coupled physical‐biogeochemical model which was designed to examine the seasonal and interannual variability of nutrients and phytoplankton dynamics in the Changjiang Estuary over the period of 1999–2016. The variations of nutrient source from the Changjiang Estuary in the last 18 years had been identified. The model demonstrated that this estuary ecosystem had a rapid response to the changes in riverine nutrients. The total nutrient concentrations, as well as their fluxes of the system, had similar variation patterns with river discharge, indicating that the river was the principal source of nutrients for the nearshore and offshore regions in that area. The phytoplankton population in terms of the ratio between diatoms and dinoflagellates responded quickly to changes in river nutrient fluxes. Key Points: Physical and biogeochemical models have been coupled to study pelagic planktonic ecosystem variability in a river estuary systemConsequences of changing nutrient fluxes over the last 18 years into the estuary on nutrient biogeochemistry and plankton were studiedPelagic ecosystem responded rapidly to river discharge and nutrient flux but exhibited different patterns for nutrients and phytoplankton [ABSTRACT FROM AUTHOR]